Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “hydrogen bonds”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.

Lin, Jiusheng [University of Nebraska, Lincoln, NE↗
DOE OSTI2023

Hydrogen Bond Network Disruption by Hydration Layers in Water Solutions with Salt and Hydrogen-Bonding Polymers (PEO)

A mean field theory model describing the interaction of ion hydration layers with the network of hydrogen bonds of both water and the nonionic polymer poly(ethylene oxide) (PEO) is presented. The predictions of the model for types and statistics of hydrogen bonds, the number of water molecules bound to PEO, or their dependence on temperature are successfully verified from all-atom simulations at different NaCl and PEO concentrations. Furthermore, our simulations show that the binding of cations to PEO increases monotonically with salt concentration, in agreement with recent experimental results, through a mechanism in which the sum of the number of bound water and cations is independent of salt concentration. Here, the model introduced is general and can describe any salt or hydrogen-bond-forming polymer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Resolving the Impact of Hydrogen Bonding on the Phylloquinone Cofactor through Two-Dimensional Infrared Spectroscopy

Phylloquinone (PhQ) is a molecule involved in photosynthetic electron transfer, where the local protein environment is known to tune the properties of PhQ through various noncovalent interactions. In this work, we determine how hydrogen bonding, one of these noncovalent interactions, alters the vibrational potential energy surface of PhQ. In addition, this work demonstrates how hydrogen bonding to PhQ manifests in ultrafast multidimensional vibrational spectra, which is an important step towards using ultrafast vibrational based spectroscopies to probe PhQ embedded in the binding pocket of photosynthetic reaction centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure

Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. Here, we show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Extending Badger's rule. I. The relationship between energy and structure in hydrogen bonds

Here, we derive a new expression for the strength of a hydrogen bond (V HB ) in terms of the elongation of the covalent bond of the donor fragment participating in the hydrogen bond (Δr HB ) and the intermolecular coordinates R (separation between the heavy atoms) and θ (deviation of the hydrogen bond from linearity). The expression includes components describing the covalent D–H bond of the hydrogen bond donor via a Morse potential, the Pauli repulsion, and electrostatic interactions between the constituent fragments using a linear expansion of their dipole moment and a quadratic expansion of their polarizability tensor. We fitted the parameters of the model using ab initio electronic structure results for six hydrogen bonded dimers, namely, NH 3 –NH 3 , H 2 O–H 2 O, HF–HF, H 2 O–NH 3 , HF–H 2 O, and HF–NH 3 , and validated its performance for extended parts of their potential energy surfaces, resulting in a mean absolute error ranging from 0.07 to 0.31 kcal/mol. The derived expression describes the energy–structure relationship in terms of a single structural parameter, namely, the elongation of the donor’s covalent bond (Δr HB ), and suggests the novel relationship of 8.0 kcal/mol pm −1 (or 0.8 kcal/mol per 0.001 Å elongation). This structural parameter is easily obtained from theory and can serve as the single descriptor of the strength of individual hydrogen bonds.

Santis, Garrett D. [Univ. of Washington, Seattle, ↗
DOE OSTI2024

Hydrogen Bonding in Amorphous Indomethacin

Amorphous Indomethacin has enhanced bioavailability over its crystalline forms, yet amorphous forms can still possess a wide variety of structures. Here, Empirical Potential Structure Refinement (EPSR) has been used to provide accurate molecular models on the structure of five different amorphous Indomethacin samples, that are consistent with their high-energy X-ray diffraction patterns. It is found that the majority of molecules in amorphous Indomethacin are non-bonded or bonded to one neighboring molecule via a single hydrogen bond, in contrast to the doubly bonded dimers found in the crystalline state. The EPSR models further indicate a substantial variation in hydrogen bonding between different amorphous forms, leading to a diversity of chain structures not found in any known crystal structures. The majority of hydrogen bonds are associated with the carboxylic acid group, although a significant number of amide hydrogen bonding interactions are also found in the models. Evidence of some dipole–dipole interactions are also observed in the more structurally ordered models. The results are consistent with a distribution of Z-isomer intramolecular type conformations in the more disordered structures, that distort when stronger intermolecular hydrogen bonding occurs. The findings are supported by 1H and 2H NMR studies of the hydrogen bond dynamics in amorphous Indomethacin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Quasi-one-dimensional hydrogen bonding in nanoconfined ice

Abstract The Bernal-Fowler ice rules stipulate that each water molecule in an ice crystal should form four hydrogen bonds. However, in extreme or constrained conditions, the arrangement of water molecules deviates from conventional ice rules, resulting in properties significantly different from bulk water. In this study, we employ machine learning-driven first-principles simulations to identify a new stabilization mechanism in nanoconfined ice phases. Instead of forming four hydrogen bonds, nanoconfined crystalline ice can form a quasi-one-dimensional hydrogen-bonded structure that exhibits only two hydrogen bonds per water molecule. These structures consist of strongly hydrogen-bonded linear chains of water molecules that zig-zag along one dimension, stabilized by van der Waals interactions that stack these chains along the other dimension. The unusual interplay of hydrogen bonding and van der Waals interactions in nanoconfined ice results in atypical proton behavior such as potential ferroelectric behavior, low dielectric response, and long-range proton dynamics.

Science & Technology - Other Topics↗
DOE OSTI2024

Disentangling Acid‐Base Chemistry through Blue Shifting Hydrogen Bond Contributions

The blue shifting of vibrational frequencies in hydrogen bonded molecules, as observed in aqueous environments, has been attributed to local partial charge transfer from solvation. Here, in this study, we extrapolate the blue shift model to the stronger ionic interactions between hydrogen bond acceptors associated with protonation through augmented pH levels and competitive interactions with counter ion pairing. The chemical model we utilize in this work is the aqueous pyridine‐pyridinium equilibrium to characterize the blue shifts observed in the pyridinium chloride ionic system. The observed agreement between observed experimental and calculated spectral shifts shows that the blue shifting model can be extrapolated to stronger interactions and accurately describe the nature of the hydrogen bond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Hydrogen-Bond-Promoted Planar Conformation, Crystallinity, and Charge Transport in Semiconducting Diazaisoindigo Derivatives

Conformational control of π-conjugated molecules using intramolecular noncovalent bonds represents a promising strategy to tailor the solid-state molecular packing and electronic properties of these materials. Here, we report the design and synthesis of two model compounds featuring intramolecular hydrogen bonds formed between a center diazaisoindigo unit (the acceptor) and flanking indole units (the donor). Computational and experimental investigations show that these hydrogen bonds enthalpically stabilize the coplanar molecular conformation by over 10 kcal/mol. The formation of these hydrogen bonds is also slightly favorable in terms of entropy, ensuring high temperature stability of the planar conformation. In this work, thermal annealing of thin films of these compounds imparts high crystallinity and orientation in the solid state, while the non-hydrogen bond control only gave an amorphous solid. Field-effect transistor devices fabricated from these thin films exhibit hole mobilities up to 0.270 cm 2 V -1 s -1 , in contrast to the lack of measurable charge carrier mobility for the non-hydrogen bond control. This work demonstrates an efficient synthetic strategy to incorporate robust intramolecular hydrogen bonds into conjugated π-systems and elucidates the mechanism on how such hydrogen bonds promote the desired molecular conformation, solid-state packing, and electronic performances of conjugated organic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Enhancing Substrate–Metal Catalyst Affinity via Hydrogen Bonding: Pd(II)-Catalyzed β-C(sp 3 )–H Bromination of Free Carboxylic Acids

Achieving sufficient substrate-metal catalyst affinity is a fundamental challenge for developing synthetically useful C–H activation reactions of weakly coordinating native substrates. While hydrogen bonding has been harnessed to bias site selectivity in existing C(sp 2 )–H activation reactions, the potential for designing catalysts with hydrogen bond donors (HBDs) to enhance catalyst substrate affinity, and thereby facilitate otherwise unreactive C(sp 3 )–H activation, remains to be demonstrated. Herein, we report the discovery of a ligand scaffold containing a remote amide motif that can form a favorable meta-macrocyclic hydrogen bonding interaction with the aliphatic acid substrate. The utility of this ligand scaffold is demonstrated through the development of an unprecedented C(sp 3 )–H bromination of α-tertiary and α-quaternary free carboxylic acids, which proceeds in exceedingly high mono-selectivity. Furthermore, the geometric relationship of the NHAc hydrogen bond donor and the coordinating quinoline ligand is crucial for forming the meta-macrocyclophane-like hydrogen bonding interaction, providing a guideline for the future design of catalysts employing secondary interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Tailoring the Selective Oxidation of Hydroxyl-Containing Compounds via Precisely Tuning the Hydrogen-Bond Strength of Catalyst H-Bond Acceptors

The unique performance of the enzyme is mainly achieved via weak interactions between the “outer coordination sphere” and the substrate. Inspired by this process, we developed 3D encapsulated-structure catalysts with hydrogen-bond engineering on the shell, which mimics the “outer coordination sphere” of an enzyme. Various hydrogen bond acceptors (C=O, S=O, and N–O groups) are imparted in the shell. Concentration-dependent 1H NMR, inverse-phase gas Chromatography (IGC) measurements, and DFT calculations underscore that the hydrogen bond strength between the acceptor groups and alcohol follows the order of C=O < S=O < N–O. The hydroxyl compound oxidation rate vs the hydrogen bond strength follows a volcano behavior, reminiscent of Sabatier’s principle. The performance variation among catalysts is attributed to the adsorption strength of the substrate. The proposed bioinspired design principle expands the scope of encapsulated catalysts, enabling fine regulation of catalytic activity through precise microenvironment control via weak interactions with substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Crystal Engineering of Hydrogen Bonding for Direct Air Capture of CO2: A Quantum Crystallography Perspective

Rising atmospheric CO2 levels demand efficient and sustainable carbon capture solutions. Direct air capture (DAC) via crystallizing hydrogen-bonded frameworks such as carbonate salts has emerged as a promising approach. This review explores the potential of crystal engineering, in tandem with advanced quantum crystallography techniques and computational modeling, to unlock the full potential of DAC materials. We examine the critical role of hydrogen bonding and other noncovalent interactions within a family of bis-guanidines that governs the formation of carbonate salts with high CO2 capture capacity and low regeneration energies for utilization. Quantum crystallography and charge density analysis prove instrumental in elucidating these interactions. A case study of a highly insoluble carbonate salt of a 2,6-pyridine-bis-(iminoguanidine) exemplifies the effectiveness of these approaches. However, challenges remain in the systematic and precise determination of hydrogen atom positions and atomic displacement parameters within DAC materials using quantum crystallography, and limitations persist in the accuracy of current energy estimation models for hydrogen bonding interactions. Future directions lie in exploring diverse functional groups, designing advanced hydrogen-bonded frameworks, and seamlessly integrating experimental and computational modeling with machine learning. This synergistic approach promises to propel the design and optimization of DAC materials, paving the way for a more sustainable future.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Hydrogen bond–induced aqueous-phase surface modification of nanocellulose and its mechanically strong composites

Aqueous-phase surface modification of nanocellulose is desirable because nanocellulose is generally produced via water-based fibrillation. In this study, a hydrogen bond–induced surface modification of cellulose nanofibrils (CNFs) in water was developed. Tannic acid and polyvinylpyrrolidone were chosen to modify the CNFs because of their strong capacity for hydrogen bond formation. By tuning the hydrogen bond formation between CNFs, tannic acid, and polyvinylpyrrolidone, CNFs with different surface hydrophilicity were achieved. Additionally, the modified CNFs can assemble into strong and tough composites owing to the hydrogen bond network in the system. Modified CNFs demonstrated 76% higher tensile strength and 100% higher toughness than those of unmodified CNFs, reaching 162 MPa and 12.7 MJ/m 3 , respectively. This study provides a new water-based modification strategy for the nanocellulose, leading the way toward producing strong nanocellulose composites via noncovalent interaction.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Isolating solvent–solute hydrogen bonding interactions via 2D IR solvation shell spectroscopy

The solvation shell around a solute is a fundamental feature of liquid-phase solutions, determining the behavior and properties of both the solute and the overall solution. Direct experimental measurements of the solvation shell properties are challenging due to the strong signals generated from the bulk solvent, which overwhelm the small contribution of the solvation shell. Here, we use ultrafast two dimensional infrared (2D IR) spectroscopy and intermolecular cross-peaks to isolate the IR absorption spectrum of methanol molecules in the solvation shell surrounding the solute N-methylacetamide. We demonstrate that the intermolecular coupling between the solvent and solute vibrations is indirectly mediated by a low-frequency hydrogen-bonding mode, suggesting an important mechanism for anharmonic coupling induced by hydrogen bonds. From the relative frequency shifts and cross-peak anisotropy, we find that methanol molecules surrounding N-methylacetamide form stronger and distinctly oriented hydrogen bonds than those in the bulk solvent. Here, we also compare these results with the solvent spectra of the solute N,N-dimethylacetamide to investigate how solute structural changes alter the solvation shell and the contribution of N–H hydrogen bond donation. Our results are supported by molecular dynamics simulations, which provide detailed insights into the hydrogen-bonding distributions. Through these results, we demonstrate 2D solvation shell spectroscopy to be a valuable method for investigating solvation structures and dynamics without interference from the bulk solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Manipulation of intramolecular hydrogen bonds in conjugated pseudoladder polymer for semiconductivity and solution-processability

The conformational coplanarity and local rigidity of π-conjugated backbones are critical for the semiconducting performance of organic electronic materials. The conformational coplanarity and local rigidity of π-conjugated backbones are critical for the semiconducting performance of organic electronic materials. While fusing the aromatic system into a ladder-type structure effectively enhances these properties, it also often results in poor solution processability and hence limits their transition to device application. To address this challenge, an intramolecularly hydrogen-bonded pseudoladder polymer (HPLP) system based on alternating hydrogen bond donating benzobisimidazole (BBI) and hydrogen bond accepting benzodifuran (BDF) units, is designed and synthesized. A Boc-protected precursor of HPLP allows for feasible solution processing of the polymer into thin films. Subsequently, in situ thermal Boc-deprotection generates the HPLP polymer, in which intramolecular hydrogen bonds form between each pair of neighboring repeating units, inducing coplanarity and rigidity throughout the entire backbone. This process is accompanied by a significant red-shift of the absorption spectrum, reduced bandgap, and enhanced rigidity, as confirmed by NMR, UV-Vis, and density functional theory analyses. HPLP films exhibit a three-order-of-magnitude enhancement in charge carrier mobility compared to the Boc-protected precursor and demonstrate excellent solvent resistance in organic thin-film transistors.

Miranda, Octavio↗
DOE OSTI2025

Hydrogen Bond Benchmark: Focal‐Point Analysis and Assessment of DFT Functionals

We performed a hierarchical, convergent ab initio benchmark study and systematically analyzed the performance of density functional approximations for describing hydrogen bonds in small neutral, cationic, and anionic complexes, as well as in larger systems involving amide, urea, deltamide, and squaramide moieties. Focal point analyses (FPA), extrapolating to the ab initio limit, were carried out using correlated wave function methods up to CCSDT(Q) for the small complexes and CCSD(T) for the larger systems, together with correlation-consistent Gaussian basis sets up to the complete basis set limit. Optimized geometries and vibrational frequencies were obtained at the CCSD(T) level. The resulting FPA hydrogen-bond energies converge within a few tenths of a kcal mol −1 . These reference data were used to evaluate 60 density functionals (including 12 dispersion-corrected), spanning the local-density approximation (LDA), generalized gradient approximations (GGAs), meta-GGAs, hybrids, meta-hybrids, double-hybrids, and range-separated hybrids. Overall, the meta-hybrid M06-2X provides the best performance for both hydrogen bond energies and geometries, while the dispersion-corrected GGAs BLYP-D3(BJ) and BLYP-D4 also yield accurate hydrogen-bond data and can serve as cost-effective options for studying large and complex systems.

coupled cluster theory↗